On 2011-12-12 09:54, sulatha M. S wrote:
Dear David,

    Yes it is DGact.
    The DGeq follows from the fraction of COOH that are not forming
    hydrogen bonds, option -nhbdist.


So, I need to use the equation (9) and (10) from your paper to calculate
the equilibrium constant and free energy of H-bonding.
Yes.



        Another question I have is, for a polycarboxylic acid system in
        water
        (COOH groups as side chains) for a 10ns run, I got the following
        as the
        output where the life time of the H-bond (between the polyacid and
        water) is negative. Is this correct?

    This means that the ACF has not equilibrated and you need much
    longer sims. You probably got a warning about it.


I did not get a warning here. I also have simulations (20ns) of
copolyacids where again it gave me negative life time. These runs are
well equilibrated with respect to energy and Rg of the polymers. The
system is a 20 repeat unit chain in approx. 5500 water molecules. I have
done simulations in which 10 units are COO- and the remaining 10 as COOH
along the chain. With a 10ns trajectory, the average life time of
H-bonds is positive.Only in the case of unionized acid I am getting a
negative life time.

Did you look at the ACF graph? It could be constant at 1 or 0.

    ACF 22057/22057
    Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
    Hydrogen bond thermodynamics at T = 298.15 K
    Fitting parameters chi^2 =  0.0146697
    Q =          0
    --------------------------------------------------
    Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
    Forward        -0.271     -3.687    -666.000   0.0146697
    Backward       -2.291     -0.437    -666.000
    One-way         0.101      9.882      10.207
    Integral        0.034     29.376      12.907
    Relaxation      0.063     15.803      11.370


    Thankyou for any help,

    Dr. M. S. Sulatha
    Dept. of Chemical Engineering
    IIT-Madras
    India




    --
    David van der Spoel, Ph.D., Professor of Biology
    Dept. of Cell & Molec. Biol., Uppsala University.
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    What is the value for free energy of H-bonding.






--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
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